The ‘heritability’ of domestication and its functional partitioning in the pig

We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regressio...

本研究提出一种估算方法：当以野生/家养状态作为目标表型时，可通过全基因组标记回归计算可解释方差占比（即基因组遗传力（genomic heritability））。该方法与标准Fst有所不同，可通过通用形式考量个体间的遗传相似性。我们将该策略应用于来自亚洲与欧洲的47头野猪与家猪的完整基因组数据。当我们将总基因组方差划分为基于注释定义的单核苷酸多态性（single nucleotide polymorphisms, SNPs）子集相关的组分时，发现9566个潜在有害非同义突变（non-synonymous mutations）所解释的遗传方差，与全部2500万个SNPs的总遗传方差相当。这表明，相较于调控突变与其他类型突变，驯化过程对蛋白质序列的影响程度更为显著。通路导向分析显示，卵巢类固醇生成（ovarian steroidogenesis）通路与瘦素信号（leptin signaling）通路在驯化过程中具有高度相关性。本基因组回归……